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Background: Kawasaki disease (KD) is a systemic vasculitis that predominantly affects medium-sized arteries. In addition to well-known coronary artery aneurysms (CAAs), peripheral systemic artery aneurysms (SAAs) have also been sporadically reported. In the literatures, SAAs occurred mainly in untreated, intravenous immunoglobin (IVIG)-resistant, or severe refractory KD, and thrombotic events in SAA were rarely reported.Case presentation: A 10-month-old boy with history of KD was referred to our hospital for suspected pseudoaneurysm of the axillary arteries. Four months prior to presentation, he had recurrent fever, conjunctival congestion, and rash. On the 10th day of fever echocardiography showed biliteral CAAs. He was then diagnosed with KD and given IVIG 2g/kg and aspirin at a local hospital. His fever and symptoms soon subsided and he was discharged with low dose aspirin and dipyridamole. One month prior to presentation, his parents incidentally palpated swellings in his axillae bilaterally. On admission, physical examination revealed a pulsatile swelling in his right axilla and a non-pulsatile swelling in the left. His left brachial and radial pulses were not palpable, while the pulses of other three limbs were normal. His left upper limb was cooler and less active compared to the right. Ultrasound examination revealed bilateral giant axillary artery aneurysms (AAAs) with massive thrombus in the left. Angiography confirmed bilateral giant AAAs with left AAAs completely embolized and fine collateral vessels connecting to the distal brachial artery, in addition to bilateral multiple giant CAAs without stenoses. The patient was given intravenous prostaglandin for ten days to allow for formation of collateral circulation, as well as aspirin, low molecular weight heparin (which was switched to warfarin before discharge) and metoprolol. At discharge, the temperature and movement of his left upper limb improved significantly. On follow-up at three months, his left limb improved and was similar to the right with no cardiovascular event having occurred. The images of CAAs and AAAs on ultrasound and computerized tomography remained the same.Conclusions: This case highlights the importance of evaluating peripheral SAAs in KD patients with CAA, even if their clinical course appears uncomplicated. For both large non-aortic SAAs and CAAs in KD patients, antithrombotic therapy is of utmost importance.